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Added VEP consequence header global #230

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Merged
ch-kr merged 4 commits into from
Jun 9, 2020
Merged

Added VEP consequence header global #230

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1656d5c
Added VEP consequence header global
ch-kr Jun 3, 2020
9a1746c
Added new constant VEP_CSQ_FIELDS
ch-kr Jun 3, 2020
8de3aec
Updated VEP_CSQ_FIELDS
ch-kr Jun 4, 2020
cc6360b
Added note about vep csq header to changelog
ch-kr Jun 9, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,7 @@

## Unreleased

* Added `VEP_CSQ_HEADER` to generate vep description necessary for VCF export. [(#230)](https://github.com/broadinstitute/gnomad_methods/pull/230)
* Modified variant QC pipeline functions `generate_trio_stats` and `generate_sib_stats` to add filter parameter for autosomes and bi-allelic sites [(#223)](https://github.com/broadinstitute/gnomad_methods/pull/223)
* `score_bin_agg` now requires additional annotations `ac` and `ac_qc_samples_unrelated_raw` and no longer needs `tdt` [(#223)](https://github.com/broadinstitute/gnomad_methods/pull/223)
* Changed `score_bin_agg` to use `ac_qc_samples_unrelated_raw` annotation instead of `unrelated_qc_callstats` [(#223)](https://github.com/broadinstitute/gnomad_methods/pull/223)
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19 changes: 12 additions & 7 deletions gnomad/utils/vep.py
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Expand Up @@ -74,6 +74,17 @@
}


VEP_CSQ_FIELDS = "Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|ALLELE_NUM|DISTANCE|STRAND|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoF|LoF_filter|LoF_flags|LoF_info"
"""
Constant that defines the order of VEP annotations used in VCF export.
"""

VEP_CSQ_HEADER = f"Consequence annotations from Ensembl VEP. Format: {VEP_CSQ_FIELDS}"
"""
Constant that contains description for VEP used in VCF export.
"""


def vep_context_ht_path(ref: str = "GRCh37"):
if ref not in VEP_REFERENCE_DATA.keys():
raise DataException(
Expand Down Expand Up @@ -264,13 +275,7 @@ def filter_vep_to_synonymous_variants(


def vep_struct_to_csq(
vep_expr: hl.expr.StructExpression,
csq_fields: str = "Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|"
"HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|"
"ALLELE_NUM|DISTANCE|STRAND|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|"
"TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|"
"HGVS_OFFSET|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoF|LoF_filter|"
"LoF_flags|LoF_info",
vep_expr: hl.expr.StructExpression, csq_fields: str = VEP_CSQ_FIELDS
) -> hl.expr.ArrayExpression:
"""
Given a VEP Struct, returns and array of VEP VCF CSQ strings (one per consequence in the struct).
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